I have long questioned the assumption that most genomic DNA sequences are “nonsensical” or “junk.” And given the data that have emerged over the past seven or so years, a functionalist view of genome has robust empirical support. It is for this reason that I think many of the arguments presented by the Biologos Foundation are “wrong on many counts,” to borrow a phrase from Darrel Falk.
Here is an example. While reading the “critique” of Steve Meyer’s book, Signature in the Cell, by Francisco Ayala, a number struck me that I know to be incorrect. The integer that I am referring to is “25,000” and it is claimed to be the known tally of genes in our chromosomes:
The human genome includes about twenty-five thousand genes and lots of other (mostly short) switch sequences…
Now, the problem with such a statement is this: While there are ~25,000 protein-coding genes in our DNA, the number of RNA-coding genes is predicted to be much higher, >450,000.1 Some of the latter range in length from being quite short–only 20 or so genetic letters–to being millions of letters long. Since 2004 we have learned that over 90% of our DNA is transcribed into RNA sequences at some developmental stage, in different cell and tissue types.2, 3, 4 (Our brain cells are unusually rich in these non-translated RNAs.) These RNAs are then processed into regulatory and structural sequences of all sizes.2, 3, 4
It could of course be argued, as it has been, that most of these RNA transcripts are themselves junk. But a host of them are packaged into complexes with different proteins.1
So the true number of genes in our DNA is probably >450,000 + 25,000 = >475,000. What is more, these >450,000 genes cover more than 88.5% of our 3 billion genetic letters. That’s right–most, if not close to all, of our chromosomal DNA consists of different types of genes that have only recently been discovered.
How do these facts square with this comment made by Falk?
but this still doesn’t negate the fact that almost certainly much, if not most, of the DNA plays no role, and in many cases can be harmful.
Well, it all depends on how he is using the words “much” and “most.” I really don’t know. So I have a question for him: Exactly what fraction of the transcribed 88.5% of our DNA are you willing to say “plays no role” or can be harmful? All I am asking for is a prediction, such as “90% of these DNA letters is superfluous” (“or 79.5% of the RNAs are nonsensical”). Since he also said “almost certainly” in the above statement, he must have a figure in mind. So I say pick a number, any number…But to be a good sport, I’ll show my prediction: All of the expressed 88.5% of our DNA has diverse roles in our development.
1 Rederstorff M, Bernhart SH, Tanzer A, Zywicki M, Perfler K, Lukasser M, Hofacker IL, Hüttenhofer A. 2010 (In Press). RNPomics: Defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles. Nucleic Acids Research.
2 Amaral PP, Dinger ME, Mercer TR, Mattick JS. 2008. The eukaryotic genome as an RNA machine. Science 319(5871): 1787-1789;
3 Dinger ME, Amaral PP, Mercer TR, Mattick JS. 2009. Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Briefings in Functional Genomics and Proteomics 8(6): 407-423;
4 Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS, Mehler MF. 2010. Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neuroscience 11(1): 14.